NEW: We changed the default behavior of save_tmp (now False). Pass --save_tmp for retrocompatibility
NEW: We changed the default beavior of save_panda_results. Now all PANDA outputs have column headers by default. Pass old_compatible for the previous behavior
Input data:
Expression: tcga_coad_cms4.nodot.txt
Motif data: /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt
PPI data: /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt
Start Panda run ...
Loading motif data ...
  Elapsed time: 2.90 sec.
Loading expression data ...
  Elapsed time: 0.33 sec.
Loading PPI data ...
Number of PPIs: 138479
  Elapsed time: 0.05 sec.
Calculating coexpression network ...
  Elapsed time: 4.39 sec.
Creating motif network ...
  Elapsed time: 3.77 sec.
Creating PPI network ...
  Elapsed time: 0.11 sec.
intersection /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt tcga_coad_cms4.nodot.txt /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt False False False
Normalizing networks ...
  Elapsed time: 26.37 sec.
Running PANDA algorithm ...
Computing panda on CPU
step: 0, hamming: 3.7393558944586207
step: 1, hamming: 0.769130745002207
step: 2, hamming: 0.616611490761829
step: 3, hamming: 0.5526802952924741
step: 4, hamming: 0.504467699183333
step: 5, hamming: 0.45962778717651726
step: 6, hamming: 0.41567950373221
step: 7, hamming: 0.37263153360912593
step: 8, hamming: 0.33113154787143967
step: 9, hamming: 0.291868519737118
step: 10, hamming: 0.2553754420179092
step: 11, hamming: 0.22198394512707917
step: 12, hamming: 0.19183910584850936
step: 13, hamming: 0.164935946151247
step: 14, hamming: 0.14115947708943063
step: 15, hamming: 0.12032110117635153
step: 16, hamming: 0.10218833286607346
step: 17, hamming: 0.08650738683683164
step: 18, hamming: 0.07301963460349725
step: 19, hamming: 0.061472944470427296
step: 20, hamming: 0.051629012971870655
step: 21, hamming: 0.043267657369531004
step: 22, hamming: 0.036188941122708464
step: 23, hamming: 0.030213789509983803
step: 24, hamming: 0.02518357820121298
step: 25, hamming: 0.0209590682487424
step: 26, hamming: 0.017418974116397826
step: 27, hamming: 0.014458330895377788
step: 28, hamming: 0.011986804549977574
step: 29, hamming: 0.009927030971327609
step: 30, hamming: 0.00821303667913851
step: 31, hamming: 0.006788774348181992
step: 32, hamming: 0.0056067909460477735
step: 33, hamming: 0.0046270317002547814
step: 34, hamming: 0.0038157791711977166
step: 35, hamming: 0.0031447209860937285
step: 36, hamming: 0.0025901368664207943
step: 37, hamming: 0.0021321945408065784
step: 38, hamming: 0.001754343444016193
step: 39, hamming: 0.0014427952559691055
step: 40, hamming: 0.0011860807715403548
step: 41, hamming: 0.0009746734154756808
Running panda took: 725.83 seconds!
Saving PANDA network to panda_tcga_coad_cms4.txt ...
WARNING: panda is now saved with the column names. 
Use old_compatible=True to save the panda results as previous versions without header
  Elapsed time: 45.66 sec.
